The X-Men's Kitsune
by alexa-catta123
Summary: I hope to figure out a better title. It all started with Apocalypse traveling through the time streams. But it ended with a different Naruto than anyone would expect. Enemies are friends, and nothing is what it seems. Enjoy.


**Here is a new Crossover. I read something similar a few years ago. And wanted to try my own version. Note this story has been hiding in my USB for a few years while i try to finish. Thought I would post to see what others think.**

**(Bold words): Author speaking in the story.**

"People talking in story"

_'People thinking in story'_

_::Telepathic Speaking::_

**_::Kyuubi Speaking::_**

**Prologue Part One: Konoha overview**

**Now this Konoha is different from from the cannon version. In it, Danzo was killed early on for trying a rebellion against the Hokage a few months after the start of the story, so no ROOT ANBU. The Uchiha's failed rebellion still happened but only the elders and some of the head house was killed, though not by Itachi since he was still too young to be in the ANBU, he is only two years older than his brother in this story. And the children of the new generation otherwise known as the Rookie 10 (Sai is with the group from the beginning), the Suna siblings, and four others (Itachi being one of the older group) were chosen for a new way to teach. Along with their senseis but this will be introduced later in the story.**

**The Elemental Nations also does exist in our earth, but somehow it has its own dimension like many people say the legendary place Avalon does. Inside the elemental nations, the edge of their dimension looks to be a never-ending mountain chain, while outside of it, looks the same. Only the ones who know what to look for can find the elemental nations.**

**Some things unfortunately did not change. Naruto is still the Kyuubi no Kitsune's carrier and is hated by the villagers, and many of shinobi of the village. He is still treated like dirt. But this young child tried to hide his pain from those he considered his precious people. Naruto is only around four years of age and already he is targeted by beings who want to use him as a weapon.**

**And here is where the story changes…**

**Prologue Part 2: The New Story**

**-THREE YEARS AGO-**

Unknown to one-year-old Naruto, the young boy was being watched by two evil beings, one thousands of years old while the other is younger than his companion but just as evil. They watch the child waiting for the perfect time to strike the child. They wait to see if he can become their "perfect weapon". Few years after his birth, they decide it is time and collect him.

Though the boy does have an ally against the two. The Kyuubi no Kitsune whom deeply regretted his actions from years ago, vowed that he would forever protect his young jailer. He already started by enhancing his charge's healing abilities, his five senses, and his learning ability, now the child is able to learn by watching others teach their charges, since many teachers are only willing to teach him the wrong things in hoping to make the child fail. Kyuubi also gave his jailer a photographic memory, and other abilities that we will find out about later.

**-A FEW YEARS LATER -**

In a training area of Konoha, the Village hidden in the Leaves we see a small group of four men, two who look to be wearing costumes. With them was an unconscious, and injured child around four years of age. He was a few inches smaller than his age mates, malnourished, and severely underweight; with bright blonde hair, and deep ocean blue eyes, though right now, the hair was dirty with dried blood, and the eyes were closed. The young boy was wearing a monstrosity called a neon orange jumpsuit, and he had what looked to be six whisker marks on his cheeks, three on each. Normally he is a happy child, or at least he pretends to be. So good that he sometimes even fools himself. Only around his 'precious people' can one see him truly happy.

The four people were Danzo, (both looking like in the cannon, but younger) a member of his ROOT and two others. The other two were called Apocalypse, and Mr. Sinister.

"Are you sure about this master?" asked Mr. Sinister looking at the seven-foot plus man next to him after studying the child in the ROOT's arms.

"Of course this young child will be the down fall of my enemies, after his training and a few modifications of course, he will secure my place as God." Stated the other man laughing manically, making the two shinobi shudder with fear. "To thank you Danzo, for helping me secure the last piece to my plan, I will give you advice. Attack in three months, I guarantee that if you do it will change this village. Now Mr. Sinister pick up our new possession and let us leave here." And with that, the two beings vanish, leaving Danzo and his companion plotting.

But unknown to the whole time the four were talking they were being watched by three young boys. Two of which were wearing normal civilian clothes, while the third was wearing a mini version of the ROOT ANBU uniform. The names for these three were Itachi, Sasuke, and Sai. They were all friends with Naruto, and were distraught to know that the one person in the village they considered a true friend was taken away from them. As soon as Danzo and his friend left all three nodded to each other and ran towards the Hokage Tower, to tell the one person they knew who would be worried about their friend, what they saw.

**End Prologue.**

**Chapter 1: The Conversation between Demon, and savior.**

**-ONE YEAR LATER or PRESENT TIME-**

::_HELP ME! Please Jiji, Tachi, Sa'ke, Sai, ANYONE! HELP ME!::_

Deep within the X Mansion, a thirty-six year old, man shoots out of a deep sleep when he hears the agonizing mental cry. _::Where are you? Who are you?:: _he yells trying to instinctively help the young voice filled with pain.

_::You can hear me? PLEASE HELP ME! PLEASE! DONT LEAVE ME! HELP ME!::_ yells the voice, sounding like it was a boy younger than the four seven-year-olds, Scott, Jean, Remy, and Rouge who have been living with the man for the last three years.

_::Calm down… please tell me who are you?::_

_::You will help me, not leave right?::_

_::I promise.::_

_::Kyuu-san says my name is Naruto and he says I am five years old… You won't leave us right? The men told me that Jiji, Tachi, Sa'ke, and Sai gave me to them. You won't leave right? PLEASE DON'T LEAVE!:: _he sounded so desperate, and lost_._

_::Kyuu-san?:: _asks the man; while he gets up, hoping to keep the young boy talking, and keep him calm as well. 'five years old and already such a strong telepath.' Thinks the man while moving towards the main computer Cerebro, hoping to find where the boy is.

_::Uh-huh, he is my friend, though he sometimes acts like he is dead when the men come. He will also take over if it becomes too much, he is letting me talk to you now, but I am getting sleepy… You'll help us right? You won't leave?.:: _asks the young boy sounding very scared and worried.

_::I will not leave you. Tell me Naruto, why do you need help?::_

_::Because the men will not leave me alone, they are hurting me! Please you will help me right?!::_

_::__**Perhaps I should talk to the man, my kit. You need to rest. The men are gone.:: **_comes a strange voice, this voice sounds both evil and good, but instinctively the man could tell that this voice will do anything for the child.

_::And who are you?:: _asks the man while activating Cerebro.

_**::It is polite to give your name first before asking for someone else's.::**_comes back the strange voice.

_::My name is Professor Charles Xavier, or just Professor X. I am a telepath like our young friend. Now may you tell me who you are?::_

_**::My name is Kyuubi no Kitsune, or just plain Kyuubi. But I will not tell you my, or my kit's history without your help escaping first. Even though he is at rest, the memories will be too much for him right now.::**_ stating the voice sounding worried, and tired at the same time.

_::But how do I find where you are?:: _asks Xavier, sensing that Kyuubi and Naruto will be vanishing from his mind soon.

_**::You are acquaintances with a man that goes by the name of Magneto. Correct?:: **_asks Kyuubi growing fainter.

_::Yes, we used to be best friends until our ideals changed. Do you mean he can sense where you are?::_

_**::Yes when we become within his range though… The men holding Naruto have many different kinds of metal here. Once you are able to sense our general location ask him to find the area that has mass quantities of different kinds of metal, much more than what is natural. That is where we are. Once you get here, I will tell you how to find the room we are in.::**_

_::Alright, but may you tell me who has done this to him?::_ asks Xavier, dreading the answer.

_**::You already know who is at fault, the main person, or should I say monster, is one of your oldest enemies. Please come soon, neither me nor my kit will be able to stay conscious for long. And the monster stated as soon as we finally lose consciousness he would begin 'the conditioning'… Whatever that is.::**_ states the voice becoming almost too faint to be heard now.

When Xavier heard of this, he yelled out, _::Whatever you do, Kyuubi do not. REPEAT DO NOT! Lose consciousness, when you do your 'kit' will be turned into a brainless beast, only listening to his master!::_

_**::Thank you for the warning Xavier, I will keep conscious until I feel you and your friends nearby, and we are safe. Please make sure both you and Magneto have at least two people each. Farewell you are our last hope, please do not let us down.:: **_with these last few words the voice left Xavier's head.

"Cerebro have you found the source of the mental energy?" asks Xavier a few minutes later, while waiting for Wolverine and Storm appear after Cerebro alerted them of a new mutant signature.

"Area confirmed to be within a ten square mile radius, the area is in the Pacific ocean, no known islands or land masses detected within the radius." Reports a female computer voice. While this is happening in walks a man and woman. The man is around 5' 10" tall with black hair in a strange style, he is heavily muscled, but not enough that it overwhelms him. The woman had long white hair and brown skin the color of an espresso.

"Professor did Cerebro find a new mutant signature?" asks the woman, while her companion reads the computer screen.

"Yes it did Storm." Answers Xavier while trying to figure out how to contact Erik or Magneto as he is called.

"Doc, this thin' states that it found the location using you as a focal point. Wha' gives?" states the man after a few moments of silence.

"Well Wolverine…"

After explaining to his two companions about the conversation he had with the boy and his protector, both Storm and Wolverine stated that they would be going with him and Magneto to save Naruto.

**End Chapter One**

**Chapter Two: Apocalypse's Plans.**

**-A FEW DAYS LATER-**

"I still do not know how you convinced me to help you Charles." Admits a man walking next to Xavier who is in his wheelchair. The man was wearing what looked like red body armor, and he had a cape and a red helmet on his head. The four companions spreading out to make sure that there was no surprises waiting.

"Simple Erik, we both agreed that Apocalypse has went too far this time, experimenting on children is a line neither of us will allow to be crossed." Stated his companion.

"Sigh… you are correct my old friend. But understand this. The Brotherhood and I still have our own point of view. And unless you find something that will change it, we will be back to enemies after this."

"Agreed. Do you sense the room our charge is in?"

"Yes I do, this Kyuubi character was correct in stating that there is only one room in this place with a large amount of adamantium in it. The room is around fifty feet ahead of us."

With that, the two became quiet and walked to the door, and hopefully the young one they are here to rescue.. But when Xavier tried to open the door, it was locked. Magneto just looked at the door than it started to compact within itself. When it was done, the two went into the room. There they saw what looked to be a small lab with computers along one wall and in the middle was a large tube filled with strange green-grey liquid. Placed inside the liquid was a young boy around five years of age, he looked to be in a deep sleep.

_**::So you have arrived Xavier, and you have brought help. I need to thank you for coming so quickly. If you and your companion will like more information on my kit just use the computer closest to him. I believe that the monster has stored all of his stats and everything on it.::**_

_::Thank you Kyuubi. Now rest we will be getting you and your kit out soon.::_ after the conversation Xavier turns towards Magneto and beckons him to follow. "I believe that this computer has the answers we seek."

When they open up the computer, the two men see a hologram of a third being appeared over the computer screen. This man was the being they feared to be, Apocalypse. The other four walked in when the hologram started to speak.

**Kyuubi File accessed.** States the hologram. **Beginning of File named "Alternate Life" started, afterwards will detail the Four-Year Plan File, than a list of genetic changes. This is a recorded version of my project to make the ultimate army. The young boy in the tube is called Naruto Uzumaki. He is from this world's Elemental Nations. A pocket dimension found deep in the arctic, around 100 square miles north of the nation of Japan. **

**This is not the same Elemental Nations that I have first met Naruto Uzumaki, nor the same person. I have met the grown version in an alternate time stream. The adult was strong, far stronger than I have anticipated. He is able to do techniques that they call jutsus with no problem. **Here Apocalypse's hologram changed to show a thirty-something year old Naruto making hand signs than a large fireball flew from his mouth.

**This Naruto also was an expert on hand to hand combat, and using multiple types of weapons. **While Apocalypse was talking the hologram changed to show the adult Naruto fighting with, and without weapons.

**He also was able to summon different sized toads to help him in battle. **Once again, it changed to show Naruto sitting on top of a toad the size of a skyscraper, and another that had him fighting along side an adult human male sized toad.

**So I decided to see if I can find a way to use this time streams Naruto Uzumaki for my own purposes.**

**The Naruto of our timeline I found out was supposed to have a decent childhood. Unlike the version I have met, which overcame great challenges to become the great warrior he was when i met him. This older Naruto was even too much for Mr. Sinister to conquer. He was to be adopted into a prestigious clan and grow to be one of the strongest shinobi or ninja in his time or the past. Thus, I decided to change this one's future and use him for my own purposes. End file "Alternate Life".**

"Oh my lord," stated Xavier when he heard this, "That monster will use a young boy that had a good life planned for him and just take it away…"

"I understand Charles. But at least he will receive assistance from the X-Men and Brotherhood from now on to help him." Answered Magneto after a few moments. "Now let's hear the rest of his plans so we know how to help Naruto."

"Of course." With this said, Xavier opened the next file on the computer. The same hologram of Apocalypse appeared announcing that the file named "**Four-Year Plan" has been activated.**

**At the beginning, I did not know how to change this Naruto's fate. Than a stroke of luck happened and I stumbled upon a power hungry shinobi by the name of Danzo. Using him, I managed to stop the clan that wanted to adopt the boy from being able to, and was able to commence the beatings that will jump start the boy's remarkable healing ability.**

**When my test subject was four years of age, I decided it is time to start experimenting. And had Danzo beat the child to near death than bring him to me. Afterwards I started finding mutations in the elemental nations to add to the boys DNA. While changing the subjects DNA, I will also begin conditioning him to be my perfect weapon.**

**The DNA alternations will be finished a year after acquiring Naruto, than the true conditioning will begin. End of file labeled "Four-Year Plan".**

"I am going to play the rest while we wait for the others. Is this alright Erik?"

"That is fine Charles, but let's make sure to make copies of the files as well."

**Beginning file labeled 'Additions to the Plan and the BLL'. While searching for mutations I found nine other children his age, four that are two years older, and four adults that have great potential to help with my Four-Year Plan a.k.a the Kyuubi Plan. All of the potential lived in his village called Konoha or Village hidden in the Leaves. I found three other children, siblings and they are the children of the leader, in a different village called Suna that I will add to the mix as well. I have decided to allow the changes to be gradual, but they will be the first wave after my Perfect Weapon, that will bring the universe to its knees before me. My basic plan is that I shall change their DNA in a way that once they reach the age of fifteen their mutations will begin to grow out of control, and since the Xavier Institute for the Gifted will not be able to locate them, I shall offer my services and then let's just say the rest will be history. They will go through a diluted version of my Perfect Weapon's conditioning. Enough that will make them obedient but not enough that they will be too powerful for him to kill them if necessary.**

**So without them, their parents or even Danzo's knowledge I changed their DNA and increased the potential of their mutations or as the elemental nations call them Bloodline Limits. According to my research, the mutations have been happening for generations, thus a few generations ago they stabilized and became Bloodline Limit (BLL). I believe that if the non-mutants do not kill the mutants off in the regular world we will also gain BLL's.**

**Now for Naruto, he does not have any known BLL, but he does have the Kyuubi no Kitsune. Or Nine-Tailed Fox Demon. The demon was sealed into the boy at birth and is already affecting his DNA, and how the energy the Elemental Nations called chakra is used by the boy. I was unable to find scientific information on this 'chakra' and believe it is a simple manifestation of the mental or psychic energy of this world. End file "Additions to the Plan and the BLL".**

"At least we know to keep an eye to the elemental nations for the next few years."

"I agree. Charles… When this group is ready I would like you to train them." Came the surprising reply.

"Why Erik? You can help them as good as I can. Maybe even better, since they are trained in the ways of fighting."

"Exactly my old friend. I would like them to enjoy their childhood, and being a teenager. Not make them into soldiers before they are used to their powers. This includes young Naruto. He will be raised by you and your X-Men primarily not by me and my Brotherhood, though we will help. After all you have the best chance at helping him learn control, and have a loving home."

"Very well my friend I will agree with you. Now let's open the next file. After this one our group should be finished and arrive here."

**Opening file named "Abilities and Genetic manipulation" **announces the hologram of Apocalypse. **When I first started to study the Kyuubi experiment…**

"This must be what he calls Naruto…" states Xavier.

**I was surprised on how quick the boy healed the wounds that Danzo inflicted on him. Wounds that would have taken a normal person at least a month to heal from, took him only a few days. I decided to experiment how much pain the boy could accept before losing consciousness. This was so I know how much will be needed to break him later. Surprisingly the Kyuubi experiment was able to last around three weeks of constant human torture before finally fainting from the pain, all this without conditioning.**

**While fainting, the Kyuubi experiment was also able to sink into a deep subconscious state. From here it looked like the demon sealed in the boy was awake. A few weeks and several dozen 'sessions' later the demon tried to escape the seal on the boy, ultimately leading to the demon's demise. Thus leaving the experiment with the demon's energy. Where the rest of the Demon vanished I do not care. But the Experiment is still living."**

"That is enough for now. We must get Naruto back to the mansion for Hank to look at him. Erik can you copy the information they have on our young charge and than destroy this place?" While asking Professor X and Wolverine deactivated and destroyed the machine holding Naruto."

"It Will be my pleasure Charles. I shall meet all of you back at the airplane."

**-End Chapters-**

**So what you guys think. a little tweaking heere and there and ready to be viewed. If I get anymore inspiration I will try to add. Thank you.**


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